1.
Heterocyclic compound
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A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different elements as members of its ring. Heterocyclic chemistry is the branch of chemistry dealing with the synthesis, properties. Examples of heterocyclic compounds include all of the acids, the majority of drugs, most biomass. Although heterocyclic compounds may be inorganic, most contain at least one carbon, while atoms that are neither carbon nor hydrogen are normally referred to in organic chemistry as heteroatoms, this is usually in comparison to the all-carbon backbone. But this does not prevent a compound such as borazine from being labelled heterocyclic, IUPAC recommends the Hantzsch-Widman nomenclature for naming heterocyclic compounds. Heterocyclic compounds can be classified based on their electronic structure. The saturated heterocycles behave like the acyclic derivatives, thus, piperidine and tetrahydrofuran are conventional amines and ethers, with modified steric profiles. Therefore, the study of heterocyclic chemistry focuses especially on unsaturated derivatives, included are pyridine, thiophene, pyrrole, and furan. Another large class of heterocycles are fused to rings, which for pyridine, thiophene, pyrrole, and furan are quinoline, benzothiophene, indole. Fusion of two benzene rings gives rise to a large family of compounds, respectively the acridine, dibenzothiophene, carbazole. The unsaturated rings can be classified according to the participation of the heteroatom in the pi system, heterocycles with three atoms in the ring are more reactive because of ring strain. Those containing one heteroatom are, in general, stable and those with two heteroatoms are more likely to occur as reactive intermediates. Five-membered rings with one heteroatom, The 5-membered ring compounds containing two heteroatoms, at least one of which is nitrogen, are called the azoles. Thiazoles and isothiazoles contain a sulfur and an atom in the ring. A large group of 5-membered ring compounds with three heteroatoms also exists, one example is dithiazoles that contain two sulfur and a nitrogen atom. Five-member ring compounds with four heteroatoms, With 5-heteroatoms, the compound may be considered rather than heterocyclic. With 7-membered rings, the heteroatom must be able to provide an empty pi orbital for normal aromatic stabilization to be available, otherwise, for example, with the benzo-fused unsaturated nitrogen heterocycles, pyrrole provides indole or isoindole depending on the orientation. The pyridine analog is quinoline or isoquinoline, for azepine, benzazepine is the preferred name

2.
Organic chemistry
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Study of structure includes many physical and chemical methods to determine the chemical composition and the chemical constitution of organic compounds and materials. In the modern era, the range extends further into the table, with main group elements, including, Group 1 and 2 organometallic compounds. They either form the basis of, or are important constituents of, many products including pharmaceuticals, petrochemicals and products made from them, plastics, fuels and explosives. Before the nineteenth century, chemists generally believed that compounds obtained from living organisms were endowed with a force that distinguished them from inorganic compounds. According to the concept of vitalism, organic matter was endowed with a vital force, during the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and he separated the different acids that, in combination with the alkali, produced the soap. Since these were all compounds, he demonstrated that it was possible to make a chemical change in various fats, producing new compounds. In 1828 Friedrich Wöhler produced the chemical urea, a constituent of urine, from inorganic starting materials. The event is now accepted as indeed disproving the doctrine of vitalism. In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkins mauve and his discovery, made widely known through its financial success, greatly increased interest in organic chemistry. A crucial breakthrough for organic chemistry was the concept of chemical structure, ehrlich popularized the concepts of magic bullet drugs and of systematically improving drug therapies. His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums, early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds, the development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the methods developed by Adolf von Baeyer. In 2002,17,000 tons of indigo were produced from petrochemicals. In the early part of the 20th Century, polymers and enzymes were shown to be large organic molecules, the multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of natural compounds increased in complexity to glucose. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones, since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12

3.
Chemical compound
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A chemical compound is an entity consisting of two or more atoms, at least two from different elements, which associate via chemical bonds. Many chemical compounds have a numerical identifier assigned by the Chemical Abstracts Service. For example, water is composed of two atoms bonded to one oxygen atom, the chemical formula is H2O. A compound can be converted to a different chemical composition by interaction with a chemical compound via a chemical reaction. In this process, bonds between atoms are broken in both of the compounds, and then bonds are reformed so that new associations are made between atoms. Schematically, this reaction could be described as AB + CD → AC + BD, where A, B, C, and D are each unique atoms, and AB, CD, AC, and BD are each unique compounds. A chemical element bonded to a chemical element is not a chemical compound since only one element. Examples are the diatomic hydrogen and the polyatomic molecule sulfur. Chemical compounds have a unique and defined chemical structure held together in a spatial arrangement by chemical bonds. Pure chemical elements are not considered chemical compounds, failing the two or more atom requirement, though they often consist of molecules composed of multiple atoms. There is varying and sometimes inconsistent nomenclature differentiating substances, which include truly non-stoichiometric examples, from chemical compounds, other compounds regarded as chemically identical may have varying amounts of heavy or light isotopes of the constituent elements, which changes the ratio of elements by mass slightly. Characteristic properties of compounds include that elements in a compound are present in a definite proportion, for example, the molecule of the compound water is composed of hydrogen and oxygen in a ratio of 2,1. In addition, compounds have a set of properties. The physical and chemical properties of compounds differ from those of their constituent elements, however, mixtures can be created by mechanical means alone, but a compound can be created only by a chemical reaction. Some mixtures are so combined that they have some properties similar to compounds. Other examples of compound-like mixtures include intermetallic compounds and solutions of metals in a liquid form of ammonia. Compounds may be described using formulas in various formats, for compounds that exist as molecules, the formula for the molecular unit is shown. For polymeric materials, such as minerals and many metal oxides, the elements in a chemical formula are normally listed in a specific order, called the Hill system

4.
Double bond
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A double bond in chemistry is a chemical bond between two chemical elements involving four bonding electrons instead of the usual two. The most common double bond, that is two carbon atoms, can be found in alkenes. Many types of double bonds exist between two different elements, for example, in a carbonyl group with a carbon atom and an oxygen atom. Other common double bonds are found in azo compounds, imines and sulfoxides, in skeletal formula the double bond is drawn as two parallel lines between the two connected atoms, typographically, the equals sign is used for this. Double bonds were first introduced in chemical notation by prominent Russian chemist Alexander Butlerov, double bonds involving carbon are stronger than single bonds and are also shorter. Double bonds are also electron-rich, which makes them reactive, the type of bonding can be explained in terms of orbital hybridization. In ethylene each carbon atom has three sp2 orbitals and one p-orbital, the three sp2 orbitals lie in a plane with ~120° angles. The p-orbital is perpendicular to this plane, when the carbon atoms approach each other, two of the sp2 orbitals overlap to form a sigma bond. At the same time, the two p-orbitals approach and together form a pi-bond. For maximum overlap, the p-orbitals have to parallel, and, therefore. This property gives rise to cis-trans isomerism, double bonds are shorter than single bonds because p-orbital overlap is maximized. With 133 pm, the ethylene C=C bond length is shorter than the C−C length in ethane with 154 pm. The double bond is stronger,636 kJ mol−1 versus 368 kJ mol−1. In an alternative representation, the double bond results from two overlapping sp3 orbitals as in a bent bond, in molecules, with alternating double bonds and single bonds, p-orbital overlap can exist over multiple atoms in a chain, giving rise to a conjugated system. Conjugation can be found in such as dienes and enones. In cyclic molecules, conjugation can lead to aromaticity, in cumulenes, two double bonds are adjacent. Double bonds are common for period 2 elements carbon, nitrogen, and oxygen, metals, too, can engage in multiple bonding in a metal ligand multiple bond. Double bonded compounds, alkene homologs, R2E=ER2 are now known for all of the heavier group 14 elements, unlike the alkenes these compounds are not planar but adopt twisted and/or trans bent structures

5.
Aromaticity
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Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, since the most common aromatic compounds are derivatives of benzene, the word “aromatic” occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group, the earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of compounds, many of which have odors. In terms of the nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the pi system to be delocalized around the ring, increasing the molecules stability. The molecule cannot be represented by one structure, but rather a hybrid of different structures. These molecules cannot be found in one of these representations, with the longer single bonds in one location. Rather, the molecule exhibits bond lengths in between those of single and double bonds and this commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds, was developed by August Kekulé. The model for benzene consists of two forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a stable molecule than would be expected without accounting for charge delocalization. As is standard for resonance diagrams, the use of an arrow indicates that two structures are not distinct entities but merely hypothetical possibilities. Neither is a representation of the actual compound, which is best represented by a hybrid of these structures. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon–carbon bonds have the same length, intermediate between that of a single and that of a double bond. In a cyclic molecule with three alternating double bonds, cyclohexatriene, the length of the single bond would be 1.54 Å. However, in a molecule of benzene, the length of each of the bonds is 1.40 Å, a better representation is that of the circular π-bond, in which the electron density is evenly distributed through a π-bond above and below the ring

6.
Pyrrole
–
Pyrrole is a heterocyclic aromatic organic compound, a five-membered ring with the formula C4H4NH. It is a volatile liquid that darkens readily upon exposure to air. Substituted derivatives are also called pyrroles, e. g. N-methylpyrrole, porphobilinogen, a trisubstituted pyrrole, is the biosynthetic precursor to many natural products such as heme. Pyrroles are components of more complex macrocycles, including the porphyrins of heme, the chlorins, bacteriochlorins, chlorophyll, Pyrrole is a colorless volatile liquid that darkens readily upon exposure to air, and is usually purified by distillation immediately before use. Pyrrole is a 5-membered aromatic heterocycle, like furan and thiophene, unlike furan and thiophene, it has a dipole in which the positive end lies on the side of the heteroatom, with a dipole moment of 1.58 D. In CDCl3, it has chemical shifts at 6.68 and 6.22, Pyrrole is weakly basic, with a conjugate acid pKa of −3.8. The most thermodynamically stable pyrrolium cation is formed by protonation at the 2 position, Substitution of pyrrole with alkyl substituents provides a more basic molecule—for example, tetramethylpyrrole has a conjugate acid pKa of +3.7. Pyrrole is also weakly acidic at the N–H position, with a pKa of 17.5, Pyrrole was first detected by F. F. Runge in 1834, as a constituent of coal tar. In 1857, it was isolated from the pyrolysate of bone and its name comes from the Greek pyrrhos, from the reaction used to detect it—the red color that it imparts to wood when moistened with hydrochloric acid. Pyrrole itself is not naturally occurring, but many of its derivatives are found in a variety of cofactors, other pyrrole-containing secondary metabolites include PQQ, makaluvamine M, ryanodine, rhazinilam, lamellarin, prodigiosin, myrmicarin, and sceptrin. The syntheses of pyrrole-containing haemin, synthesized by Emil Fischer was recognized by the Nobel Prize, Pyrrole is a constituent of tobacco smoke and not as an ingredient. Pyrrole is prepared industrially by treatment of furan with ammonia in the presence of acid catalysts, like SiO2. Pyrrole can also be formed by dehydrogenation of pyrrolidine. Several syntheses of the ring have been described. The Hantzsch pyrrole synthesis is the reaction of β-ketoesters with ammonia, the Knorr pyrrole synthesis involves the reaction of an α-amino ketone or an α-amino-β-ketoester with an activated methylene compound. The method involves the reaction of an α-aminoketone and a compound containing a methylene group α to a carbonyl group, in the Paal–Knorr pyrrole synthesis, a 1, 4-dicarbonyl compound reacts with ammonia or a primary amine to form a substituted pyrrole. The Van Leusen reaction can be used to form pyrroles, by reaction of tosylmethyl isocyanide with an enone in the presence of base, a 5-endo cyclization then forms the 5-membered ring, which reacts to eliminate the tosyl group. The last step is tautomerization to the pyrrole, the Barton–Zard synthesis proceeds in a manner similar to the Van Leusen synthesis

7.
Hydrogenation
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Hydrogenation – to treat with hydrogen – is a chemical reaction between molecular hydrogen and another compound or element, usually in the presence of a catalyst such as nickel, palladium or platinum. The process is employed to reduce or saturate organic compounds. Hydrogenation typically constitutes the addition of pairs of atoms to a molecule. Catalysts are required for the reaction to be usable, non-catalytic hydrogenation takes place only at high temperatures. Hydrogenation reduces double and triple bonds in hydrocarbons and it has three components, the unsaturated substrate, the hydrogen and, invariably, a catalyst. The reduction reaction is carried out at different temperatures and pressures depending upon the substrate, the same catalysts and conditions that are used for hydrogenation reactions can also lead to isomerization of the alkenes from cis to trans. This process is of great interest because hydrogenation technology generates most of the fat in foods. A reaction where bonds are broken while hydrogen is added is called hydrogenolysis, some hydrogenations of polar bonds are accompanied by hydrogenolysis. For hydrogenation, the source of hydrogen is H2 gas itself. The hydrogenation process often uses greater than 1 atmosphere of H2, usually conveyed from the cylinders, gaseous hydrogen is produced industrially from hydrocarbons by the process known as steam reforming. For many applications, hydrogen is transferred from donor molecules such as acid, isopropanol. These hydrogen donors undergo dehydrogenation to, respectively, carbon dioxide, acetone and these processes are called transfer hydrogenations. Typical substrates are listed in the table With rare exceptions, H2 is unreactive toward organic compounds in the absence of metal catalysts, the unsaturated substrate is chemisorbed onto the catalyst, with most sites covered by the substrate. In heterogeneous catalysts, hydrogen forms surface hydrides from which hydrogens can be transferred to the chemisorbed substrate, platinum, palladium, rhodium, and ruthenium form highly active catalysts, which operate at lower temperatures and lower pressures of H2. Non-precious metal catalysts, especially based on nickel have also been developed as economical alternatives. The trade-off is activity vs. cost of the catalyst and cost of the apparatus required for use of high pressures, notice that the Raney-nickel catalysed hydrogenations require high pressures, Catalysts are usually classified into two broad classes, homogeneous catalysts and heterogeneous catalysts. Homogeneous catalysts dissolve in the solvent that contains the unsaturated substrate, heterogeneous catalysts are solids that are suspended in the same solvent with the substrate or are treated with gaseous substrate. Some well known homogeneous catalysts are indicated below and these are coordination complexes that activate both the unsaturated substrate and the H2

8.
Imine
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An imine is a functional group or chemical compound containing a carbon–nitrogen double bond. The Nitrogen atom can be attached to a hydrogen or an organic group, if this group is not a hydrogen atom, then the compound can sometimes be referred to as a Schiff base. The carbon atom has two single bonds. Usually imines refer to compounds with the connectivity R2C=NR, as discussed below, in the older literature, imine refers to the aza analogue of an epoxide. Thus, ethyleneimine is the ring species C2H4NH. Imines are related to ketones and aldehydes by replacement of the oxygen with an NR group, when R = H, the compound is a primary imine, when R is hydrocarbyl, the compound is a secondary imine. Imines exhibit diverse reactivity and are encountered throughout chemistry. When R3 is OH, the imine is called an oxime, a primary imine in which C is attached to both a hydrocarbyl and a H is called a primary aldimine, a secondary imine with such groups is called a secondary aldimine. A primary imine in which C is attached to two hydrocarbyls is called a primary ketimine, an imine with such groups is called a secondary ketimine. One way of naming aldimines is to take the name of the radical, remove final e, see the aldimine article for other naming conventions. N-Sulfinyl imines are a class of imines having a sulfinyl group attached to the nitrogen atom. In recent years, several such as Trisborate, pyrrolidine or Titanium Ethoxide have been shown to catalyse imine formation. Several other methods exist for the synthesis of imines, reaction of organic azides with metal carbenoids. Condensation of carbon acids with nitroso compounds, the rearrangement of trityl N-haloamines in the Stieglitz rearrangement. By reaction of alkenes with hydrazoic acid in the Schmidt reaction, by reaction of a nitrile, hydrochloric acid, and an arene in the Hoesch reaction. Multicomponent synthesis of 3-thiazolines in the Asinger reaction, primary ketimines can be synthesized via a Grignard reaction with a nitrile. The most important reactions of imines are their hydrolysis to the corresponding amine, otherwise this functional group participates in many other reactions, many of which are analogous to the reactions of aldehydes and ketones. An imine is reduced in reductive amination, an imine reacts with an amine to an aminal, see for example the synthesis of cucurbituril

9.
Amine
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In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group, important amines include amino acids, biogenic amines, trimethylamine, and aniline, see Category, Amines for a list of amines. Inorganic derivatives of ammonia are also called amines, such as chloramine, see Category, compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. An aliphatic amine has no aromatic ring attached directly to the nitrogen atom, aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents, the presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect. Amines are organized into four subcategories, Primary amines — Primary amines arise when one of three atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, Secondary amines — Secondary amines have two organic substituents bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine, tertiary amines — In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a fishy smell. Cyclic amines — Cyclic amines are either secondary or tertiary amines, examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of tertiary amines. It is also possible to have four organic substituents on the nitrogen and these species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions, Amines are named in several ways. Typically, the compound is given the prefix amino- or the suffix, the prefix N- shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine, triamine, tetraamine, systematic names for some common amines, Hydrogen bonding significantly influences the properties of primary and secondary amines. Thus the melting point and boiling point of amines is higher than those of the corresponding phosphines, for example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic smell, liquid amines have a distinctive fishy smell. The nitrogen atom features a lone pair that can bind H+ to form an ammonium ion R3NH+

10.
Aroma compound
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An aroma-compound, also known as an odorant, aroma, fragrance, or flavor, is a chemical compound that has a smell or odor. A chemical-compound has a smell or odor when it is volatile to be transported to the olfactory system in the upper-part of the nose. Generally molecules meeting this specification have molecular weights of <300, flavors affect both the sense of taste and smell, whereas fragrances affect only smell. Flavors tend to be occurring, and fragrances tend to be synthetic. Aroma-compounds can be found in food, wine, spices, floral scent, perfumes, fragrance oils, for example, many form biochemically during the ripening of fruits and other crops. In wines, most form as byproducts of fermentation, an odorizer may add an odorant to a dangerous odorless substance, like propane, natural gas, or hydrogen, as a safety measure. Note, Carvone, depending on its chirality, offers two different smells, furaneol 1-Hexanol cis-3-Hexen-1-ol Menthol High concentrations of aldehydes tend to be very pungent and overwhelming, but low concentrations can evoke a wide range of aromas. Acetaldehyde Hexanal cis-3-Hexenal Furfural Hexyl cinnamaldehyde Isovaleraldehyde – nutty, fruity, cocoa-like Anisic aldehyde – floral, sweet and it is a crucial component of chocolate, vanilla, strawberry, raspberry, apricot, and others. Its smell is so potent it can be detected several hundred meters downwind mere seconds after a container is opened, butane-1-thiol, commonly called normal-butyl mercaptan is a chemical-intermediate. Olfactory-receptors are cell-membrane receptors on the surface of neurons in the olfactory system that detect air-borne. In mammals, olfactory-receptors are expressed on the surface of the epithelium in the nasal cavity. In 2005–06, fragrance-mix was the third-most-prevalent allergen in patch tests, Fragrance was voted Allergen of the Year in 2007 by the American Contact Dermatitis Society. The composition of fragrances is usually not disclosed in the label of products, hiding the actual chemicals of the formula, the EPA, however, does not conduct independent-safety testing but relies on data provided by the manufacturer. In 2010 the International Fragrance Association published a list of 3,059 chemicals used in 2011 based on a voluntary-survey of its members and it was estimated to represent about 90% of the worlds production-volume of fragrances

11.
Thienamycin
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Thienamycin, one of the most potent naturally produced antibiotics known thus far, was discovered in Streptomyces cattleya in 1976. Thienamycin has excellent activity against both Gram-positive and Gram-negative bacteria and is resistant to bacterial β-lactamase enzymes, Thienamycin is a zwitterion at pH7. In 1976, fermentation broths obtained from the soil bacterium Streptomyces cattleya were found to be active in screens for inhibitors of peptidoglycan biosynthesis, initial attempts to isolate the active species proved difficult due to the chemical instability of that component. After many attempts and extensive purification, the material was finally isolated in >90% purity, Thienamycin was the first among the naturally occurring class of carbapenem antibiotics to be discovered and isolated. Carbapenems are similar in structure to their antibiotic “cousins” the penicillins, like penicillins, carbapenems contain a β-lactam ring fused to a five-membered ring. In vitro, thienamycin employs a similar mode of action as penicillins through disrupting the cell wall synthesis of various Gram-positive and Gram-negative bacteria. Although thienamycin binds to all of the proteins in Escherichia coli, it preferentially binds to PBP-1 and PBP-2. Unlike penicillins, which are rendered ineffective through rapid hydrolysis by the β-lactamase enzyme present in some strains of bacteria, Thienamycin displayed high activity against bacteria that were resistant to other β-lactamase-stable compounds, highlighting the superiority of thienamycin as an antibiotic among β-lactams. The formation of thienamycin is thought to occur through a different pathway from classic β-lactams, the gene cluster for the biosynthesis of thienamycin of S. cattleya was identified and sequenced in 2003, lending insight into the biosynthetic mechanism for thienamycin formation. The biosynthesis is thought to share features with the biosynthesis of the simple carbapenems, the β-lactam is then formed by a β-lactam synthetase, which makes use of ATP, providing a carbapenam. At some later point, oxidation to the carbapenem and ring inversions must occur, the hydroxyethyl side chain of thienamycin is thought to be a result of two separate methyl transfers from S-adenosyl methionine. According to the proposed gene functions, ThnK, ThnL, a β-lactam synthetase is thought to catalyze the formation of the β-lactam ring fused to the five-membered ring. How the cysteaminyl side-chain is incorporated is largely unknown, although ThnT, ThnR, due to low titre and to difficulties in isolating and purifying thienamycin produced by fermentation, total synthesis is the preferred method for commercial production. Numerous methods are available in the literature for the synthesis of thienamycin. One synthetic route is given in Figure 3, the starting β-lactam for the pathway given above can be synthesized using the following method, Thienamycin is extremely unstable and decomposes in aqueous solution. Consequently, it is impractical for the treatment of bacterial infections. One such derivative — imipenem — was formulated in 1985, imipenem, an N-formimidoyl derivative of thienamycin, is rapidly metabolized by a renal dipeptidase enzyme found in the human body. To prevent its degradation, imipenem is normally coadministered with cilastatin

12.
MTSL
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MTSL is a organosulfur compound that is used as an nitroxide spin label. MTSL is bifunctional, consisting of the nitroxide and the ester functional groups. The nitroxide label is sterically protected, so it is relatively unreactive, MTSL is attached to proteins by reaction with thiol groups. The reaction exploits standard reactivity of thiosulfate esters, sulfinic acid is the leaving group, RSO2S-nitroxide + protein-SH → protein-S-S-nitroxide + RSO2H The heterodisulfide bond to the cysteine residue is robust, enabling site-directed spin labelling. The MTSL moiety will add 184.3 daltons to the mass of the protein or peptide to which it is attached, the cysteine can be introduced using site-directed mutagenesis, and hence most positions in a protein can be labelled. In Nuclear magnetic resonance the introduction of the group increases the relaxation rate of nearby nuclei. Its presence can be detected as peak broadening and loss of intensity in peaks corresponding to nearby nuclei, hence proximity can be inferred for all nuclei, that are affected. Spin labelling with MTSL is frequently used in investigation of residual structure in intrinsically unstructured proteins

13.
Pyrrolysine
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Pyrrolysine is an ɑ-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacterium, it is not present in humans. It contains a group, a carboxylic acid group. Its pyrroline side-chain is similar to that of lysine in being basic, nearly all proteins are made using only 20 standard amino acid building blocks. Two unusual genetically-encoded amino acids are selenocysteine and pyrrolysine, pyrrolysine was discovered in 2002 at the active site of methyl-transferase enzyme from a methane-producing archeon, Methanosarcina barkeri. This amino acid is encoded by UAG, and its synthesis, as determined by X-ray crystallography and MALDI mass spectrometry, pyrrolysine is made up of 4-methylpyrroline-5-carboxylate in amide linkage with the ϵN of lysine. Pyrrolysine is synthesized in vivo by joining two molecules of L-lysine, one molecule of lysine is first converted to -3-methyl-D-ornithine, which is then ligated to a second lysine. An NH2 group is eliminated, followed by cyclization and dehydration step to yield L-pyrrolysine, the extra pyrroline ring is incorporated into the active site of several methyltransferases, where it is believed to rotate relatively freely. It is believed that the ring is involved in positioning and displaying the group of methylamine for attack by a corrinoid cofactor. In this way a net CH+3 is transferred to the cobalt atom with a change of oxidation state from I to III. The methylamine-derived ammonia is released, restoring the original imine. It is encoded in mRNA by the UAG codon, which in most organisms is the stop codon. The pylT and pylS genes are part of an operon of Methanosarcina barkeri, with homologues in other sequenced members of the Methanosarcinaceae family, M. acetivorans, M. mazei, pyrrolysine-containing genes are known to include monomethylamine methyltransferase, dimethylamine methyltransferase, and trimethylamine methyltransferase. Homologs of pylS and pylT have also found in an Antarctic archaeon, Methanosarcina barkeri. The occurrence in Desulfitobacterium is of special interest, because bacteria, when use of the amino acid appeared confined to the Methanosarcinaceae, the system was described as a late archaeal invention by which a 21st amino acid was added to the genetic code. Afterward it was concluded that PylRS was already present in the last universal common ancestor some 3 billion years ago, another possibility is that evolution of the system involved a horizontal gene transfer between unrelated microorganisms. The other genes of the Pyl operon mediate pyrrolysine biosynthesis, leading to description of the operon as a genetic code expansion cassette. Some differences exist between the bacterial and archaeal systems studied, homology to pylS is broken into two separate proteins in D. hafniense. Most notably, the UAG codon appears to act as a stop codon in many of that organisms proteins, by contrast, in methanogenic archaea it was not possible to identify any unambiguous UAG stop signal

14.
Proteinogenic amino acid
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Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word proteinogenic means protein creating, throughout known life, there are 22 genetically encoded amino acids,20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms. The latter often results from post-translational modification of proteins, some non-proteinogenic amino acids are incorporated into nonribosomal peptides which are synthesized by non-ribosomal peptide synthetases. In some methanogenic prokaryotes, the UAG codon can also be translated to pyrrolysine, in eukaryotes, there are only 21 proteinogenic amino acids, the 20 of the standard genetic code, plus selenocysteine. Humans can synthesize 12 of these from other or from other molecules of intermediary metabolism. The other nine must be consumed, and so they are called essential amino acids, the essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The proteinogenic amino acids have been found to be related to the set of amino acids that can be recognized by ribozyme autoaminoacylation systems, thus, non-proteinogenic amino acids would have been excluded by the contingent evolutionary success of nucleotide-based life forms. The following illustrates the structures and abbreviations of the 21 amino acids that are encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions, the masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Forming a peptide bond results in elimination of a molecule of water, general chemical properties §, Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide. The value for Arg is from Pace et al, the value for Sec is from Byun & Kang. The pKa value of Pyrrolysine has not been reported, note, The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein. Protein pKa calculations are used to calculate the change in the pKa value of an amino-acid residue in this situation. In mass spectrometry of peptides and proteins, knowledge of the masses of the residues is useful, the mass of the peptide or protein is the sum of the residue masses plus the mass of water. The residue masses are calculated from the chemical formulas and atomic weights. In mass spectrometry, ions may also one or more protons. § Monoisotopic mass The table below lists the abundance of amino acids in E. coli cells, negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. The abundance of amino acids includes amino acids in free form, the proteinogenic set used by known life on Earth appears to be arbitrarily selected by evolution, according to current knowledge, from many hundreds of possible alpha-type amino acids

15.
Porphyrin
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Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges. The parent porphyrin is porphin, and substituted porphines are called porphyrins, the porphyrin ring structure is aromatic, with a total of 26 electrons in the conjugated system. Various analyses indicate that not all atoms of the ring are involved equally in the conjugation or that the overall nature is substantially based on several smaller conjugated systems. Many porphyrins are naturally occurring, one of the best-known porphyrins is heme, the pigment in red blood cells, porphyrins are the conjugate acids of ligands that bind metals to form complexes. The metal ion usually has a charge of 2+ or 3+. A schematic equation for these syntheses is shown, H2porphyrin + 2+ → MLn−4 +4 L +2 H+ where M = metal ion, some iron-containing porphyrins are called hemes. Heme-containing proteins, or hemoproteins, are found extensively in nature, hemoglobin and myoglobin are two O2-binding proteins that contain iron porphyrins. Several other heterocycles are related to porphyrins and these include corrins, chlorins, bacteriochlorophylls, and corphins. Chlorins are more reduced, contain more hydrogen than porphyrins, and this structure occurs in a chlorophyll molecule. Replacement of two of the four subunits with pyrrolinic subunits results in either a bacteriochlorin or an isobacteriochlorin. Some porphyrin derivatives follow Hückels rule, but most do not, a benzoporphyrin is a porphyrin with a benzene ring fused to one of the pyrrole units. E. g. verteporfin is a benzoporphyrin derivative, a geoporphyrin, also known as a petroporphyrin, is a porphyrin of geologic origin. They can occur in oil, oil shale, coal. Abelsonite is possibly the only geoporphyrin mineral, as it is rare for porphyrins to occur in isolation, in plants, algae, bacteria and archaea, it is produced from glutamic acid via glutamyl-tRNA and glutamate-1-semialdehyde. The enzymes involved in this pathway are glutamyl-tRNA synthetase, glutamyl-tRNA reductase and this pathway is known as the C5 or Beale pathway. Two molecules of dALA are then combined by porphobilinogen synthase to give porphobilinogen, four PBGs are then combined through deamination into hydroxymethyl bilane, which is hydrolysed to form the circular tetrapyrrole uroporphyrinogen III. This molecule undergoes a number of further modifications, intermediates are used in different species to form particular substances, but, in humans, the main end-product protoporphyrin IX is combined with iron to form heme. Bile pigments are the products of heme

16.
Ring-closing metathesis
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The most commonly synthesized ring sizes are between 5-7 atoms, however, reported syntheses include 45- up to 90- membered macroheterocycles. These reactions are metal-catalyzed and proceed through a metallacyclobutane intermediate, RCM is a favorite among organic chemists due to its synthetic utility in the formation of rings, which were previously difficult to access efficiently, and broad substrate scope. Since the only major by-product is ethylene, these reactions may also be considered atom economic, there are several reviews published on ring-closing metathesis. In the following months, Jiro Tsuji reported a similar metathesis reaction describing the preparation of a macrolide catalyzed by WCl6, the synthetic route allowed access to dihydropyrans in high yield from readily available starting materials. In addition, synthesis of substituted pyrrolines, tetrahydropyridines, and amides were illustrated in modest to high yield, the driving force for the cyclization reaction was attributed to entropic favorability by forming two molecules per one molecule of starting material. The loss of the molecule, ethylene, a highly volatile gas. The ruthenium catalysts are not sensitive to air and moisture, unlike the molybdenum catalysts, the ruthenium catalysts, known better as the Grubbs Catalysts, as well as molybdenum catalysts, or Schrock’s Catalysts, are still used today for many metathesis reactions, including RCM. The mechanism for transition metal-catalyzed olefin metathesis has been widely researched over the past forty years, RCM undergoes a similar mechanistic pathway as other olefin metathesis reactions, such as cross metathesis, ring-opening metathesis polymerization, and acyclic diene metathesis. Since all steps in the cycle are considered reversible, it is possible for some of these other pathways to intersect with RCM depending on the reaction conditions. This mechanism has become widely accepted among chemists and serves as the model for the RCM mechanism, initiation occurs through substitution of the catalyst’s alkene ligand with substrate. This process occurs via formation of a new alkylidene through one round of cycloaddition and cycloreversion, association and dissociation of a phosphine ligand also occurs in the case of Grubbs catalysts. While the loss of ethylene is a driving force for RCM, it is also generated by competing metathesis reactions. The reaction can be under kinetic or thermodynamic control depending on the reaction conditions, catalyst. Smaller rings, between 5 and 8 atoms, are more thermodynamically favored over medium to large rings due to ring strain. Ring strain arises from abnormal bond angles resulting in a heat of combustion relative to the linear counterpart. If the RCM product contains a strained olefin, polymerization becomes more preferable through ring-opening metathesis polymerization of the newly formed olefin, RCM may be considered to have a kinetic bias if the products cannot reenter the catalytic cycle or interconvert through an equilibrium. A kinetic product distribution could lead to mostly RCM products or may lead to oligomers and polymers, with the advent of more reactive catalysts, equilibrium RCM is observed quite often which may lead to a greater product distribution. The mechanism can be expanded to include the various competing equilibrium reactions as well as indicate where various side-products are formed along the reaction pathway, increased catalyst activity also allows for the olefin products to reenter the catalytic cycle via non-terminal alkene addition onto the catalyst

17.
Pyrrolidine
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Pyrrolidine, also known as tetrahydropyrrole, is an organic compound with the molecular formula 4NH. It is a secondary amine, also classified as a saturated heterocycle. It is a liquid that is miscible with water and most organic solvents. It has an ammonia-like, but characteristic odor, in addition to pyrrolidine itself, many substituted pyrrolidines are known. Pyrrolidine is produced by treatment of 1, 4-butanediol with ammonia over an oxide catalyst, many modifications of pyrrolidine are found in natural and synthetic chemistry. The pyrrolidine ring structure is present in numerous natural alkaloids such as nicotine and hygrine and it is found in many drugs such as procyclidine and bepridil. It also forms the basis for the racetam compounds, the amino acids proline and hydroxyproline are, in a structural sense, derivatives of pyrrolidine. Its basicity is typical of other dialkyl amines, relative to many secondary amines, pyrrolidine is distinctive because of its compactness, a consequence of its cyclic structure. Pyrrolidine is used as a block in the synthesis of more complex organic compounds. It is used to activate ketones and aldehydes toward nucleophilic addition by formation of enamines

18.
Integrated Authority File
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The Integrated Authority File or GND is an international authority file for the organisation of personal names, subject headings and corporate bodies from catalogues. It is used mainly for documentation in libraries and increasingly also by archives, the GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners. The GND falls under the Creative Commons Zero license, the GND specification provides a hierarchy of high-level entities and sub-classes, useful in library classification, and an approach to unambiguous identification of single elements. It also comprises an ontology intended for knowledge representation in the semantic web, available in the RDF format